Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats

DNA trinucleotide repeats, particularly CXG, are common within the human genome. However, expansion of trinucleotide repeats is associated with a number of disorders, including Huntington disease, spinobulbar muscular atrophy and spinocerebellar ataxia1,2,3,4. In these cases, the repeat length is known to correlate with decreased age of onset and disease severity5,6. Repeat expansion of (CAG)n, (CTG)n and (CGG)n trinucleotides may be related to the increased stability of alternative DNA hairpin structures consisting of CXG-CXG triads with X-X mismatches7,8,9,10,11. Small-molecule ligands that selectively bound to CAG repeats could provide an important probe for determining repeat length and an important tool for investigating the in vivo repeat extension mechanism. Here we report that napthyridine-azaquinolone (NA, 1) is a ligand for CAG repeats and can be used as a diagnostic tool for determining repeat length. We show by NMR spectroscopy that binding of NA to CAG repeats induces the extrusion of a cytidine nucleotide from the DNA helix.

[1]  K. Nakatani.  Chemistry Challenges in SNP Typing , 2004, Chembiochem : a European journal of chemical biology.

[2]  Myron F. Goodman,et al.  Gene Targeting in Rat Embryo Fibroblasts Promoted by the Polyomavirus Large T Antigen Associated With Neurological Diseases , 1996 .

[3]  T. Kamp,et al.  Hairpin properties of single-stranded DNA containing a GC-rich triplet repeat: (CTG)15. , 1995, Nucleic acids research.

[4]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[5]  R. Sinden,et al.  Chemotherapeutic deletion of CTG repeats in lymphoblast cells from DM1 patients. , 2004, Nucleic acids research.

[6]  A. Syvänen.  Accessing genetic variation: genotyping single nucleotide polymorphisms , 2001, Nature Reviews Genetics.

[7]  A. Marquis Gacy,et al.  Trinucleotide repeats that expand in human disease form hairpin structures in vitro , 1995, Cell.

[8]  D E Wemmer,et al.  Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors , 1995, Journal of biomolecular NMR.

[9]  Akio Kobori,et al.  Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface. , 2004, Nucleic acids research.

[10]  X. Gao,et al.  Sequence specific recognition of ligand-DNA complexes studied by NMR. , 2001, Current medicinal chemistry.

[11]  Emily A. Smith,et al.  Chemically induced hairpin formation in DNA monolayers. , 2002, Journal of the American Chemical Society.

[12]  R. Wells,et al.  Hairpin Formation during DNA Synthesis Primer Realignmentin Vitro in Triplet Repeat Sequences from Human Hereditary Disease Genes* , 1997, The Journal of Biological Chemistry.

[13]  K. Nakatani,et al.  Recognition of guanine-guanine mismatches by the dimeric form of 2-amino-1,8-naphthyridine. , 2001, Journal of the American Chemical Society.

[14]  K. Fischbeck,et al.  Trinucleotide repeats in neurogenetic disorders. , 1996, Annual review of neuroscience.

[15]  K. Nakatani,et al.  The SPR sensor detecting cytosine-cytosine mismatches , 2004 .

[16]  Shinsuke Sando,et al.  Scanning of guanine–guanine mismatches in DNA by synthetic ligands using surface plasmon resonance , 2001, Nature Biotechnology.

[17]  Sybren S. Wijmenga,et al.  THE USE OF NMR METHODS FOR CONFORMATIONAL STUDIES OF NUCLEIC ACIDS , 1998 .

[18]  R. Mott,et al.  Instability of highly expanded CAG repeats in mice transgenic for the Huntington's disease mutation , 1997, Nature Genetics.

[19]  S. Warren,et al.  Genetic instabilities and hereditary neurological diseases , 1998 .

[20]  J. Penney,et al.  Trinucleotide repeat length instability and age of onset in Huntington's disease , 1993, Nature Genetics.

[21]  R. Corn,et al.  Surface plasmon resonance imaging measurements of ultrathin organic films. , 2003, Annual review of physical chemistry.

[22]  J. Stavenhagen,et al.  Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome , 1997, Molecular and cellular biology.

[23]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

[24]  J. D. Engel,et al.  Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique , 2004, Genes to cells : devoted to molecular & cellular mechanisms.

[25]  S. Warren,et al.  Trinucleotide repeat expansion and human disease. , 1995, Annual review of genetics.

[26]  D. Crothers,et al.  NMR of enzymatically synthesized uniformly 13C15N-labeled DNA oligonucleotides. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[27]  C. McMurray,et al.  DNA secondary structure: a common and causative factor for expansion in human disease. , 1999, Proceedings of the National Academy of Sciences of the United States of America.